One of those articles on motogp.com that you wish had a bit more detail. Maybe Krops will fill in the blanks.

http://www.motogp.com/en/news/2014/Comparing+engine+usage+in+2014

Scott Redding (GO&FUN Honda Gresini) and Nicky Hayden (Drive M7 Aspar) went up to their 11th engine, while Hayden’s team-mate Hiroshi Aoyama was the only rider to use his maximum 12

Were there actually 12 engines? Or is that 6 engines that were built, refreshed and sealed 12 times?

It also raises the question, if the Factory Hondas can survive only 5 engine in a season, why did the lower spec, lower stressed Open Hondas need 12?